rs10890920

Variant names:

• chr11-109002392-G-A
• rs10890920
• ENST00000526041.1:n.*73C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-109002392-G-A
• chr11-109002392-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000526041.1(ENSG00000255528):​n.*73C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,118 control chromosomes in the GnomAD database, including 19,571 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.49 (19567 hom., cov: 33)
  • Exomes 𝑓: 0.65 (4 hom.)
• Consequence: ENSG00000255528 ENST00000526041.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

ENSG00000255528 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255528	ENST00000526041.1	n.*73C>T		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73996 AN: 151980 Hom.: 19558 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.508

GnomAD4 exome AF: 0.650 AC: 13 AN: 20 Hom.: 4 AF XY: 0.611 AC XY: 11 AN XY: 18

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.487 AC: 74023 AN: 152098 Hom.: 19567 Cov.: 33 AF XY: 0.490 AC XY: 36445 AN XY: 74338

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.510

Alfa AF: 0.559 Hom.: 48541

Bravo AF: 0.474

Asia WGS AF: 0.615 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10890920; hg19: chr11-108873119;